MIR339 (microRNA 339) - Rat Genome Database
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Gene: MIR339 (microRNA 339) Homo sapiens
Analyze
Symbol: MIR339
Name: microRNA 339
RGD ID: 1345058
HGNC Page HGNC
Description: Predicted to be involved in cellular response to ethanol and cellular response to leukemia inhibitory factor.
Type: ncrna
RefSeq Status: PROVISIONAL
Also known as: hsa-mir-339; mir-339; MIRN339
RGD Orthologs
Mouse
Rat
Dog
Pig
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl71,022,933 - 1,023,026 (-)EnsemblGRCh38hg38GRCh38
GRCh3871,022,933 - 1,023,026 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3771,062,569 - 1,062,662 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3671,029,094 - 1,029,187 (-)NCBINCBI36hg18NCBI36
Celera71,030,508 - 1,030,601 (-)NCBI
Cytogenetic Map7p22.3NCBI
HuRef7978,263 - 978,356 (-)NCBIHuRef
CHM1_171,060,923 - 1,061,016 (-)NCBICHM1_1
CRA_TCAGchr7v271,117,456 - 1,117,546 (-)NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

References

References - curated
1. RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14691248   PMID:15325244   PMID:15634332   PMID:16381832   PMID:17604727   PMID:19520829   PMID:20889907   PMID:20932331   PMID:21037258   PMID:24352696   PMID:24882579   PMID:25193859  
PMID:26186881   PMID:26391641   PMID:26553360   PMID:26646931   PMID:27668319   PMID:28940895   PMID:29103767   PMID:29377618   PMID:29735550   PMID:30320397   PMID:30332417   PMID:30462625  
PMID:30599080   PMID:30683807   PMID:30858545   PMID:32380054  


Genomics

Comparative Map Data
MIR339
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl71,022,933 - 1,023,026 (-)EnsemblGRCh38hg38GRCh38
GRCh3871,022,933 - 1,023,026 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh3771,062,569 - 1,062,662 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3671,029,094 - 1,029,187 (-)NCBINCBI36hg18NCBI36
Celera71,030,508 - 1,030,601 (-)NCBI
Cytogenetic Map7p22.3NCBI
HuRef7978,263 - 978,356 (-)NCBIHuRef
CHM1_171,060,923 - 1,061,016 (-)NCBICHM1_1
CRA_TCAGchr7v271,117,456 - 1,117,546 (-)NCBI
Mir339
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm395139,355,405 - 139,355,500 (-)NCBIGRCm39mm39
GRCm385139,369,650 - 139,369,745 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl5139,369,650 - 139,369,745 (-)EnsemblGRCm38mm10GRCm38
MGSCv375139,845,604 - 139,845,699 (-)NCBIGRCm37mm9NCBIm37
Celera5136,423,656 - 136,423,751 (-)NCBICelera
Cytogenetic Map5G2NCBI
Mir339
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01217,369,002 - 17,369,097 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1217,369,002 - 17,369,097 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01219,355,865 - 19,355,960 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1217,031,514 - 17,031,609 (+)NCBICelera
Cytogenetic Map12q11NCBI
MIR339-1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl615,853,520 - 15,853,577 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1615,853,520 - 15,853,577 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
MIR339-2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1164,025,972 - 164,026,057 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11164,025,972 - 164,026,057 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21181,756,284 - 181,756,369 (-)NCBISscrofa10.2Sscrofa10.2susScr3

Position Markers
STS-N27306  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3771,062,281 - 1,062,516UniSTSGRCh37
Build 3671,028,807 - 1,029,042RGDNCBI36
Celera71,030,220 - 1,030,455RGD
Cytogenetic Map7p22.3UniSTS
HuRef7977,975 - 978,210UniSTS
CRA_TCAGchr7v271,117,168 - 1,117,403UniSTS
GeneMap99-GB4 RH Map710.29UniSTS
SHGC-32510  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh3771,062,731 - 1,062,859UniSTSGRCh37
Build 3671,029,257 - 1,029,385RGDNCBI36
Celera71,030,670 - 1,030,798RGD
Cytogenetic Map7p22.3UniSTS
CRA_TCAGchr7v271,117,614 - 1,117,742UniSTS
Stanford-G3 RH Map763.0UniSTS
NCBI RH Map735.6UniSTS
GeneMap99-G3 RH Map763.0UniSTS

miRNA Target Status

Confirmed Targets
Gene TargetMature miRNAMethod NameResult TypeData TypeSupport TypePMID
RPL10Ahsa-miR-339-3pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
BCL6hsa-miR-339-5pMirtarbaseexternal_infoqRT-PCRFunctional MTI (Weak)20932331
RANhsa-miR-339-5pMirtarbaseexternal_infoCLASHFunctional MTI (Weak)23622248
ICAM1hsa-miR-339-5pOncomiRDBexternal_infoNANA19520829

Predicted Targets
Summary Value
Count of predictions:41567
Count of gene targets:15230
Count of transcripts:33804
Interacting mature miRNAs:hsa-miR-339-3p, hsa-miR-339-5p
Prediction methods:Microtar, Miranda, Pita, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 10 2 80 2 1 1 3 19 13
Low 353 390 490 108 477 107 626 208 1055 233 351 499 12 66 373 4
Below cutoff 299 267 192 33 107 17 401 259 773 34 98 124 16 133 266

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000362153
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl71,022,933 - 1,023,026 (-)Ensembl
RefSeq Acc Id: NR_029898
RefSeq Status: PROVISIONAL
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh3871,022,933 - 1,023,026 (-)NCBI
GRCh3771,062,569 - 1,062,662 (-)RGD
Celera71,030,508 - 1,030,601 (-)RGD
HuRef7978,263 - 978,356 (-)RGD
CHM1_171,060,923 - 1,061,016 (-)NCBI
CRA_TCAGchr7v271,117,456 - 1,117,546 (-)ENTREZGENE
Sequence:
Promoters
RGD ID:6814784
Promoter ID:HG_XEF:7412
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:HeLa_S3,   K562,   Lymphoblastoid
Transcripts:NR_029768,   NR_031204,   NR_031784,   NR_032481
Position:
Human AssemblyChrPosition (strand)Source
Build 3671,028,811 - 1,029,932 (-)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 7p22.3(chr7:54185-1206119)x3 copy number gain See cases [RCV000134140] Chr7:54185..1206119 [GRCh38]
Chr7:54185..1245755 [GRCh37]
Chr7:149268..1212281 [NCBI36]
Chr7:7p22.3
uncertain significance
GRCh38/hg38 7p22.3-q36.3(chr7:54185-159282390)x1 copy number loss See cases [RCV000135401] Chr7:54185..159282390 [GRCh38]
Chr7:54185..159075079 [GRCh37]
Chr7:149268..158767840 [NCBI36]
Chr7:7p22.3-q36.3
pathogenic
GRCh38/hg38 7p22.3-15.2(chr7:54185-26827634)x3 copy number gain See cases [RCV000136557] Chr7:54185..26827634 [GRCh38]
Chr7:54185..26867253 [GRCh37]
Chr7:149268..26833778 [NCBI36]
Chr7:7p22.3-15.2
pathogenic
GRCh38/hg38 7p22.3-22.2(chr7:54185-3324143)x1 copy number loss See cases [RCV000136789] Chr7:54185..3324143 [GRCh38]
Chr7:54185..3363775 [GRCh37]
Chr7:149268..3330301 [NCBI36]
Chr7:7p22.3-22.2
pathogenic
GRCh38/hg38 7p22.3-22.1(chr7:54185-6638027)x3 copy number gain See cases [RCV000136731] Chr7:54185..6638027 [GRCh38]
Chr7:54185..6677658 [GRCh37]
Chr7:149268..6644183 [NCBI36]
Chr7:7p22.3-22.1
pathogenic
GRCh38/hg38 7p22.3(chr7:791215-1993065)x3 copy number gain See cases [RCV000136691] Chr7:791215..1993065 [GRCh38]
Chr7:830852..2032700 [GRCh37]
Chr7:797378..1999226 [NCBI36]
Chr7:7p22.3
uncertain significance
GRCh38/hg38 7p22.3-21.3(chr7:45130-7252065)x3 copy number gain See cases [RCV000137524] Chr7:45130..7252065 [GRCh38]
Chr7:45130..7291696 [GRCh37]
Chr7:140213..7258221 [NCBI36]
Chr7:7p22.3-21.3
pathogenic
GRCh38/hg38 7p22.3(chr7:54185-1331046)x1 copy number loss See cases [RCV000137163] Chr7:54185..1331046 [GRCh38]
Chr7:54185..1370682 [GRCh37]
Chr7:149268..1337208 [NCBI36]
Chr7:7p22.3
pathogenic|uncertain significance
GRCh38/hg38 7p22.3-15.3(chr7:45130-25221165)x3 copy number gain See cases [RCV000137824] Chr7:45130..25221165 [GRCh38]
Chr7:45130..25260784 [GRCh37]
Chr7:140213..25227309 [NCBI36]
Chr7:7p22.3-15.3
pathogenic
GRCh38/hg38 7p22.3(chr7:689554-2031521)x3 copy number gain See cases [RCV000138319] Chr7:689554..2031521 [GRCh38]
Chr7:729191..2071156 [GRCh37]
Chr7:695717..2037682 [NCBI36]
Chr7:7p22.3
uncertain significance
GRCh38/hg38 7p22.3-22.2(chr7:54165-3258775)x1 copy number loss See cases [RCV000142995] Chr7:54165..3258775 [GRCh38]
Chr7:54165..3298407 [GRCh37]
Chr7:149248..3264933 [NCBI36]
Chr7:7p22.3-22.2
pathogenic
GRCh38/hg38 7p22.3(chr7:45130-1298050)x1 copy number loss See cases [RCV000143341] Chr7:45130..1298050 [GRCh38]
Chr7:45130..1337686 [GRCh37]
Chr7:140213..1304212 [NCBI36]
Chr7:7p22.3
uncertain significance
GRCh38/hg38 7p22.3-22.2(chr7:45130-3406236)x3 copy number gain See cases [RCV000143175] Chr7:45130..3406236 [GRCh38]
Chr7:45130..3445868 [GRCh37]
Chr7:140213..3412394 [NCBI36]
Chr7:7p22.3-22.2
uncertain significance
GRCh38/hg38 7p22.3-15.2(chr7:43360-27196404)x3 copy number gain See cases [RCV000143586] Chr7:43360..27196404 [GRCh38]
Chr7:43360..27236023 [GRCh37]
Chr7:138443..27202548 [NCBI36]
Chr7:7p22.3-15.2
pathogenic
GRCh38/hg38 7p22.3(chr7:54185-1843584)x1 copy number loss See cases [RCV000148193] Chr7:54185..1843584 [GRCh38]
Chr7:54185..1883220 [GRCh37]
Chr7:149268..1849746 [NCBI36]
Chr7:7p22.3
pathogenic
GRCh38/hg38 7p22.3-14.1(chr7:54185-41875885)x3 copy number gain See cases [RCV000051159] Chr7:54185..41875885 [GRCh38]
Chr7:54185..41915483 [GRCh37]
Chr7:149268..41882008 [NCBI36]
Chr7:7p22.3-14.1
pathogenic
GRCh38/hg38 7p22.3-22.1(chr7:45130-5880375)x1 copy number loss See cases [RCV000052249] Chr7:45130..5880375 [GRCh38]
Chr7:45130..5920006 [GRCh37]
Chr7:140213..5886532 [NCBI36]
Chr7:7p22.3-22.1
pathogenic
GRCh38/hg38 7p22.3-q36.3(chr7:53985-159282531)x1 copy number loss See cases [RCV000052250] Chr7:53985..159282531 [GRCh38]
Chr7:53985..159075220 [GRCh37]
Chr7:149068..158767981 [NCBI36]
Chr7:7p22.3-q36.3
pathogenic
GRCh38/hg38 7p22.3(chr7:54185-1843584)x1 copy number loss See cases [RCV000052253] Chr7:54185..1843584 [GRCh38]
Chr7:54185..1883220 [GRCh37]
Chr7:149268..1849746 [NCBI36]
Chr7:7p22.3
pathogenic|likely pathogenic|conflicting data from submitters
GRCh38/hg38 7p22.3(chr7:54185-1441125)x1 copy number loss See cases [RCV000052254] Chr7:54185..1441125 [GRCh38]
Chr7:54185..1480761 [GRCh37]
Chr7:149268..1447287 [NCBI36]
Chr7:7p22.3
pathogenic
GRCh38/hg38 7p22.3-22.1(chr7:45130-6270185)x3 copy number gain See cases [RCV000053527] Chr7:45130..6270185 [GRCh38]
Chr7:45130..6309816 [GRCh37]
Chr7:140213..6276341 [NCBI36]
Chr7:7p22.3-22.1
pathogenic
GRCh38/hg38 7p22.3-15.3(chr7:53985-24361531)x3 copy number gain See cases [RCV000053528] Chr7:53985..24361531 [GRCh38]
Chr7:53985..24401150 [GRCh37]
Chr7:149068..24367675 [NCBI36]
Chr7:7p22.3-15.3
pathogenic
GRCh38/hg38 7p22.3-21.3(chr7:54185-8274834)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053529]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053529]|See cases [RCV000053529] Chr7:54185..8274834 [GRCh38]
Chr7:54185..8314464 [GRCh37]
Chr7:149268..8280989 [NCBI36]
Chr7:7p22.3-21.3
pathogenic
GRCh38/hg38 7p22.3-14.2(chr7:54185-37089712)x3 copy number gain See cases [RCV000053530] Chr7:54185..37089712 [GRCh38]
Chr7:54185..37129317 [GRCh37]
Chr7:149268..37095842 [NCBI36]
Chr7:7p22.3-14.2
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:31776 AgrOrtholog
COSMIC MIR339 COSMIC
Ensembl Genes ENSG00000199023 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000362153 ENTREZGENE
GTEx ENSG00000199023 GTEx
HGNC ID HGNC:31776 ENTREZGENE
Human Proteome Map MIR339 Human Proteome Map
miRBase MI0000815 ENTREZGENE
NCBI Gene 442907 ENTREZGENE
OMIM 615977 OMIM
PharmGKB PA164722668 PharmGKB
RNAcentral URS000003FD55 RNACentral
  URS000055B190 RNACentral
  URS000075B703 RNACentral